The Spanish playmaker returns from injury to return to the Catalan club's midfield while Javier Mascherano starts at the back alongside Gerard Pique
The midfielder replaces Thiago in the middle of the park while Cesc Fabregas is listed as a substitute, with Seydou Keita coming into the side in place of Sergio Busquets.
Javier Mascherano is the only other change from the team who lost to Getafe at the weekend with Maxwell dropping out of the matchday squad.
Mascherano will partner Gerard Pique at the centre of defence while Eric Abidal will start the game at left-back.
Barcelona are currently six points behind leaders Real Madrid and will be desperate to reduce the deficit with a win over mid-table Rayo.
Barcelona (4-3-3): Valdes, Alves, Pique, Mascherano, Abidal; Xavi, Iniesta, Keita; Sanchez, Messi, Villa
Subs: Pinto, Adriano, Thiago, Pedro, Busquets, Fabregas, Puyol
Rayo Vallecano (4-2-3-1): Cobeno; Labaka, Arribas, Jordi, Casado; Fuego, Movilla; Michu, Michel, Botelho; Lass
Subs: Dani, Tamudo, Pacheco, Delibasic, Garcia, Piti, Sueliton
More to follow...